Offline mass calibration

ABSTRACT

A method includes producing ions from one or more calibrant species and delivering the ions to a mass analyzer, and measuring a first set of mass related physical values for the ions from the one or more calibrant species. The method further includes producing ions from a sample and delivering the ions to a mass analyzer, and measuring a second mass related physical value for a first sample ion species. The first sample ion species has a mass-to-charge ratio outside of the range of the mass-to-charge ratios of the calibrant ion species. Additionally, the method includes calculating a calibration curve based on the first set of mass related physical values and second mass related physical value, and modifying at least one instrument parameter based on the calibration curve.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation under 35 U.S.C. § 120 andclaims the priority benefit of U.S. patent application Ser. No.15/079,476, filed Mar. 24, 2016, which claims the priority benefit ofU.S. Provisional patent application Ser. No. 62/138,239, filed Mar. 25,2015. The disclosures of each of the foregoing applications areincorporated herein by reference.

FIELD

The present disclosure generally relates to the field of massspectrometry including systems and methods for mass calibration.

INTRODUCTION

Mass spectrometry relies upon the measurement of physical values thatcan be related to the mass-to-charge ratio (m/z) to determine a mass ofan ionic species or a compound within a sample. High mass accuracyrequires calibration of the measured physical values against species ofknown m/z or mass. Calibration is generally accomplished with the use ofa calibration mixture that produces multiple ionic species of known m/z.However, the choice of ions suitable for use in a calibration mixturemay be limited.

From the foregoing it will be appreciated that a need exists forimproved calibration methods for mass spectrometry.

SUMMARY

In a first aspect, a method can include producing ions from one or morecalibrant species and delivering the ions to a mass analyzer, andmeasuring a first set of mass related physical values for the ions fromthe one or more calibrant species. The method can further includeproducing ions from a sample and delivering the ions to a mass analyzer,and measuring a second mass related physical value for a first sampleion species. The first sample ion species can have a mass-to-chargeratio outside of the range of the mass-to-charge ratios of the calibrantion species. Additionally, the method can include calculating acalibration curve based on the first set of mass related physical valuesfor the plurality calibrant ion species and second mass related physicalvalue for the first sample ion species, and modifying at least oneinstrument parameter based on the calibration curve.

In various embodiments of the first aspect, the mass analyzer caninclude a Fourier transform mass analyzer. In specific embodiments, theinstrument parameter can be selected from the group consisting of acoefficient relating m/z to ion frequency, a frequency range for animage current, a digitizing rate, a filter bandwidth for an imagecurrent, and any combination thereof.

In various embodiments of the first aspect, the mass analyzer caninclude a quadrupole mass analyzer or a quadrupole ion trap massanalyzer. In specific embodiments, the instrument parameter can beselected from the group consisting of an RF voltage, a DC voltage, andany combination thereof.

In various embodiments of the first aspect, the mass analyzer caninclude a time-of-flight mass analyzer. In specific embodiments, theinstrument parameter can be selected from the group consisting of acoefficient relating m/z to flight time, an acquisition time window, aflight tube clearing pulse time, and any combination thereof.

In various embodiments of the first aspect, the sample can be providedby a gas chromatographic instrument.

In various embodiments of the first aspect, the sample can be providedby a liquid chromatographic instrument.

In various embodiments of the first aspect, the method can furtherinclude providing a second sample including a second sample ion speciesto the mass spectrometer; operating the mass spectrometer using themodified instrument parameter from the calibration; and measuring athird mass related physical value for the second sample ion species.

In specific embodiments, the method can further include shifting thecalibration curve based on a measured mass-to-charge ratio of a thirdsample ion species within the second sample to account for scan specificdrifts in the calibration curve, wherein the instrument parameter is notchanged based on the shifting of the calibration curve. In specificembodiments, the second sample ion species can have a mass-to-chargeratio within the range of the mass-to-charge ratio of the first sampleion species and the mass-to-charge ratio of at least one of thecalibrant ion species.

In various embodiments of the first aspect, the first sample ion speciescan have a mass-to-charge ratio above the range of the mass-to-chargeratios of the calibrant ion species.

In various embodiments of the first aspect, the first sample ion speciescan have a mass-to-charge ratio below the range of the mass-to-chargeratios of the calibrant ion species.

In a second aspect, a mass spectrometer can include an ion sourceconfigured to form ions; a mass analyzer configured to measure a massrelated physical value for an ion; and a controller. The controller canbe configured to obtain a first set of mass related physical values forions from the one or more calibrant species; obtain a second massrelated physical value for a first sample ion species; calculate acalibration curve based on the first set of mass related physicalvalues, the second mass related physical value, and known mass-to-chargeratios of ions from the one or more calibrant species and the firstsample ion species; and modify the operation of the mass analyzer basedon the calibration curve.

In various embodiments of the second aspect, the mass analyzer caninclude a Fourier transform mass analyzer. In specific embodiments,modifying the operation of the mass analyzer can include modifying acoefficient relating m/z to ion frequency, a frequency range for animage current, a digitizing rate, a filter bandwidth for an imagecurrent, and any combination thereof.

In various embodiments of the second aspect, the mass analyzer caninclude a quadrupole mass analyzer or a quadrupole ion trap massanalyzer. In specific embodiments, modifying the operation of the massanalyzer can include modifying an RF voltage, a DC voltage, or anycombination thereof.

In various embodiments of the second aspect, the mass analyzer caninclude a time-of-flight mass analyzer. In specific embodiments,modifying the operation of the mass analyzer can include modifying acoefficient relating m/z to flight time, an acquisition time window, aflight tube clearing pulse time, or any combination thereof.

In various embodiments of the second aspect, the mass spectrometer canfurther include a gas chromatograph for supplying a sample to the ionsource.

In various embodiments of the second aspect, the mass spectrometer canfurther include a liquid chromatograph for supplying a sample to the ionsource.

In various embodiments of the second aspect, the controller can befurther configured to operate the ion source to provide a second sampleincluding a second sample ion species to the mass spectrometer; operatethe mass spectrometer using the modified instrument parameter from thecalibration; and obtain a third set of mass related physical values forthe second sample ion species. In specific embodiments, the controllercan be further configured to shift the calibration curve based on ameasured mass-to-charge ratio of a third sample ion species within thesecond sample to account for scan specific drift in the calibrationcurve, wherein the operation of the mass analyzer is not changed basedon the shifting of the calibration curve.

In various embodiments of the second aspect, first sample ion speciescan have a mass-to-charge ratio above the range of the mass-to-chargeratios of the calibrant ion species.

In various embodiments of the second aspect, first sample ion speciescan have a mass-to-charge ratio below the range of the mass-to-chargeratios of the calibrant ion species.

DRAWINGS

For a more complete understanding of the principles disclosed herein,and the advantages thereof, reference is now made to the followingdescriptions taken in conjunction with the accompanying drawings, inwhich:

FIG. 1 is a block diagram of an exemplary mass spectrometry system, inaccordance with various embodiments.

FIGS. 2A and 2B are graphs illustrating an extrapolation error when onlylow mass ions are used for calibration, in accordance with variousembodiments.

FIG. 3 is a flow diagram of an exemplary method for calibrating a massanalyzer, in accordance with various embodiments.

FIG. 4 is a flow block illustrating an exemplary computer system, inaccordance with various embodiments.

FIG. 5 is an exemplary comparison between a measured and theoretical m/zfor a set of high mass ions when calibration is limited to low masscalibration ions.

FIG. 6 is an exemplary graph of the mass errors as a function of m/zwhen calibration is limited to low mass calibration ions.

FIG. 7 is an exemplary comparison between a measured and theoretical m/zfor a set of high mass ions when calibration includes low masscalibration ions and high mass sample ions.

FIG. 8 is an exemplary graph of the mass errors as a function of m/zwhen calibration includes low mass calibration ions and high mass sampleions.

FIG. 9 is an exemplary comparison between a measured and theoretical m/zfor a set of high mass ions when calibration includes low masscalibration ions and high mass sample ions with a lock mass.

FIG. 10 is an exemplary graph of the mass errors as a function of m/zwhen calibration includes low mass calibration ions and high mass sampleions with a lock mass.

It is to be understood that the figures are not necessarily drawn toscale, nor are the objects in the figures necessarily drawn to scale inrelationship to one another. The figures are depictions that areintended to bring clarity and understanding to various embodiments ofapparatuses, systems, and methods disclosed herein. Wherever possible,the same reference numbers will be used throughout the drawings to referto the same or like parts. Moreover, it should be appreciated that thedrawings are not intended to limit the scope of the present teachings inany way.

DESCRIPTION OF VARIOUS EMBODIMENTS

Embodiments of systems and methods for mass calibration are describedherein.

The section headings used herein are for organizational purposes onlyand are not to be construed as limiting the described subject matter inany way.

In this detailed description of the various embodiments, for purposes ofexplanation, numerous specific details are set forth to provide athorough understanding of the embodiments disclosed. One skilled in theart will appreciate, however, that these various embodiments may bepracticed with or without these specific details. In other instances,structures and devices are shown in block diagram form. Furthermore, oneskilled in the art can readily appreciate that the specific sequences inwhich methods are presented and performed are illustrative and it iscontemplated that the sequences can be varied and still remain withinthe spirit and scope of the various embodiments disclosed herein.

All literature and similar materials cited in this application,including but not limited to, patents, patent applications, articles,books, treatises, and internet web pages are expressly incorporated byreference in their entirety for any purpose. Unless described otherwise,all technical and scientific terms used herein have a meaning as iscommonly understood by one of ordinary skill in the art to which thevarious embodiments described herein belongs.

It will be appreciated that there is an implied “about” prior to thetemperatures, concentrations, times, pressures, flow rates,cross-sectional areas, etc. discussed in the present teachings, suchthat slight and insubstantial deviations are within the scope of thepresent teachings. In this application, the use of the singular includesthe plural unless specifically stated otherwise. Also, the use of“comprise”, “comprises”, “comprising”, “contain”, “contains”,“containing”, “include”, “includes”, and “including” are not intended tobe limiting. It is to be understood that both the foregoing generaldescription and the following detailed description are exemplary andexplanatory only and are not restrictive of the present teachings.

As used herein, “a” or “an” also may refer to “at least one” or “one ormore.” Also, the use of “or” is inclusive, such that the phrase “A or B”is true when “A” is true, “B” is true, or both “A” and “B” are true.Further, unless otherwise required by context, singular terms shallinclude pluralities and plural terms shall include the singular.

A “system” sets forth a set of components, real or abstract, comprisinga whole where each component interacts with or is related to at leastone other component within the whole.

Mass Spectrometry Platforms

Various embodiments of mass spectrometry platform 100 can includecomponents as displayed in the block diagram of FIG. 1. In variousembodiments, elements of FIG. 1 can be incorporated into massspectrometry platform 100. According to various embodiments, massspectrometer 100 can include an ion source 102, a mass analyzer 104, anion detector 106, and a controller 108.

In various embodiments, the ion source 102 generates a plurality of ionsfrom a sample. The ion source can include, but is not limited to, amatrix assisted laser desorption/ionization (MALDI) source, electrosprayionization (ESI) source, atmospheric pressure chemical ionization (APCI)source, atmospheric pressure photoionization source (APPI), inductivelycoupled plasma (ICP) source, electron ionization source, chemicalionization source, photoionization source, glow discharge ionizationsource, thermospray ionization source, and the like.

In various embodiments, the mass analyzer 104 can separate ions based ona mass-to-charge ratio of the ions. For example, the mass analyzer 104can include a quadrupole mass filter analyzer, a quadrupole ion trapanalyzer, a time-of-flight (TOF) analyzer, an electrostatic trap (e.g.,Orbitrap) mass analyzer, Fourier transform ion cyclotron resonance(FT-ICR) mass analyzer, and the like. In various embodiments, the massanalyzer 104 can also be configured to fragment the ions using collisioninduced dissociation (CID) electron transfer dissociation (ETD),electron capture dissociation (ECD), photo induced dissociation (PID),surface induced dissociation (SID), and the like, and further separatethe fragmented ions based on the mass-to-charge ratio.

In various embodiments, the ion detector 106 can detect ions. Forexample, the ion detector 106 can include an electron multiplier, aFaraday cup, and the like. Ions leaving the mass analyzer can bedetected by the ion detector. In various embodiments, the ion detectorcan be quantitative, such that an accurate count of the ions can bedetermined.

In various embodiments, the controller 108 can communicate with the ionsource 102, the mass analyzer 104, and the ion detector 106. Forexample, the controller 108 can configure the ion source orenable/disable the ion source. Additionally, the controller 108 canconfigure the mass analyzer 104 to select a particular mass range todetect. Further, the controller 108 can adjust the sensitivity of theion detector 106, such as by adjusting the gain. Additionally, thecontroller 108 can adjust the polarity of the ion detector 106 based onthe polarity of the ions being detected. For example, the ion detector106 can be configured to detect positive ions or be configured todetected negative ions.

Calibration Method

FIG. 2A is a graph illustrating a calibration curve when using only lowmass ions from a calibrant mixture and when using the low mass ions in acalibration mixture in combination with a high mass ion from a sample.FIG. 2B is an enlargement of the circled region around the pointcorresponding to the high mass ion. The solid line is a fit of thestandard calibrant ions to equation 3. The standard calibrant ions are68.99466, 99.99306, 130.99147, 263.98656, 413.97698, and 501.97059. Atm/z 959.16751, the fit is significantly off. The dashed line is a fit ofthe standard calibrant ions plus the higher mass ion to equation 3. Thisfit has improved accuracy over the range from low mass to high mass.

FIG. 3 is a flow diagram for calibrating a mass analyzer, such as massanalyzer 104 of FIG. 1. At 302, ions can be generated from a calibrantmixture. In various embodiments, the calibrant mixture can include amultiple species of known mass which can cover a range of masses. Theions of the calibrant mixture can be analyzed by the mass analyzer at304 and a set of physical values related to the m/z can be measured.Depending on the type of mass analyzer, the mass related physical valuecan be a frequency, a time, a voltage, or the like.

In various embodiments, when using a Fourier transform mass analyzer,such as an Orbitrap or a Fourier Transform Ion Cyclotron Resonance(FTICR) mass analyzer, the m/z ratio can be related to a measuredfrequency f of an induced current caused by the oscillation of the ionin the mass analyzer. The relationship can be described using Equation1, 2, or 3 for an Orbitrap or Equation 4 for a FTICR mass analyzer.

$\begin{matrix}{{1.\mspace{31mu} \frac{m}{z}} = \frac{A}{f^{2}}} \\{{2.\mspace{31mu} \frac{m}{z}} = {\frac{A}{f^{3}} + \frac{B}{f^{2}}}} \\{{3.\mspace{31mu} \frac{m}{z}} = {\frac{A}{f^{3}} + \frac{B}{f^{2}} + \frac{C}{f} + D}} \\{{4.\mspace{31mu} \frac{m}{z}} = {\frac{A}{f} + \frac{B}{f^{2}}}}\end{matrix}$

In various embodiments, when using a quadrupole mass analyzer, such as aquadrupole mass filter or a quadrupole ion trap, the m/z ratio can berelated to a voltage V applied to the quadrupole. Additionally, therecan be a time delay between when a voltage is set and when the voltageis applied to the quadrupole and the ions respond to the change in thefield. When scanning across a mass range, it may be necessary to correctfor the response delay. In various embodiments, this can be accomplishedby introducing a voltage offset B which may be a function of scan rate.The relationship can be described using Equation 5 and the correctionfor the response delay can be described using Equation 6.

$\begin{matrix}{{5.\mspace{25mu} \frac{m}{z}} = {\frac{e}{2\pi^{2}f^{2}r_{o}^{2}}V}} \\{{6.\mspace{25mu} \frac{m}{z}} = {{A \cdot V} + B}}\end{matrix}$

In various embodiments, when using a time-of-flight mass analyzer them/z ratio can be related to a time t it takes for the ion to travel theflight path. The relationship can be described using Equations 7 and 8.

$\begin{matrix}{{7.\mspace{25mu} \frac{m}{z}} = {\frac{2e\; V_{s}}{L^{2}}t^{2}}} \\{{8.\mspace{25mu} \frac{m}{z}} = {{A \cdot t^{2}} + B}}\end{matrix}$

In various embodiments, a calibration for the physical value canoptionally be determined from the measured values and the known masses,as indicated at 306.

At 308, ions can be generated from a sample containing at least onespecies of known mass. The species of known mass can have a mass outsideof the range covered by the calibrant, either lower or higher or even inbetween. In various embodiments, the sample can be a calibration sampleused to calibrate a chromatograph, such as a gas chromatograph or aliquid chromatograph. In this way, calibration of the mass analyzer canoccur concurrently with calibration of the chromatograph. In otherembodiments, calibration of the chromatograph may occur less frequentlythan calibration of the mass analyzer, and a species known to be in asample or spiked into a sample can be used.

At 310, the mass related physical value can be measured for the ionswithin the sample, including the species of known mass. At 312, acalibration curve can be calculated for the mass related physical value.The calibration can use the set of mass related physical values measuredfor the calibrant ion species and the mass related physical valuemeasured for the species of known mass in the sample. In variousembodiments, the calibration curve can be used to determine masses ofunknown ions from the measured mass related physical value with an errorof not greater than about 10 ppm, such as not greater than about 5 ppm,such as not greater than about 2 ppm, or even not greater than about 1ppm.

At 314, the operation of the mass analyzer can be modified based on thecalibration curve. In embodiments, when using a Fourier transform massanalyzer, a coefficient relating m/z to ion frequency, a frequency rangefor an image current, a digitizing rate, a filter bandwidth for an imagecurrent, or any combination thereof can be modified based on thecalibration curve. In other embodiments, when using a quadrupole massanalyzer or a quadrupole ion trap mass analyzer, an RF voltage, a DCvoltage, or any combination thereof can be modified based on thecalibration curve. In further embodiments, when using a time-of-flightmass analyzer, a coefficient relating m/z to flight time, an acquisitiontime window, a flight tube clearing pulse time, or any combinationthereof can be modified based on the calibration curve.

At 316, ions can be generated from a second sample, and at 318, the massrelated physical value can be measured using the modified operation ofthe mass analyzer.

At 320, the mass of the ions in the second sample can be determinedbased on the calibration curve. In various embodiments, a lock mass canbe used to modify the calibration curve to further improve massaccuracy. The lock mass can be derived from a species of known masswithin the second sample and can be used to shift or rotate the curve toaccount for run specific changes in the operation of the mass analyzer.Various factors can contribute to run specific alterations to themeasured mass related physical value, such as a temperature of variouscomponents of the mass analyzer, a total number of ions within the massanalyzer, and other factors. The use of the lock mass can correct forthese run specific affects without altering the operation of the massanalyzer, and can be applied while the data is collected for the sampleand before saving the data, or can be applied after the data iscollected for the sample.

Computer-Implemented System

FIG. 4 is a block diagram that illustrates a computer system 400, uponwhich embodiments of the present teachings may be implemented as whichmay incorporate or communicate with a system controller, for examplecontroller 108 shown in FIG. 1, such that the operation of components ofthe associated mass spectrometer may be adjusted in accordance withcalculations or determinations made by computer system 400. In variousembodiments, computer system 400 can include a bus 402 or othercommunication mechanism for communicating information, and a processor404 coupled with bus 402 for processing information. In variousembodiments, computer system 400 can also include a memory 406, whichcan be a random access memory (RAM) or other dynamic storage device,coupled to bus 402 for determining base calls, and instructions to beexecuted by processor 404. Memory 406 also can be used for storingtemporary variables or other intermediate information during executionof instructions to be executed by processor 404. In various embodiments,computer system 400 can further include a read only memory (ROM) 408 orother static storage device coupled to bus 402 for storing staticinformation and instructions for processor 404. A storage device 410,such as a magnetic disk or optical disk, can be provided and coupled tobus 402 for storing information and instructions.

In various embodiments, processor 404 can include a plurality of logicgates. The logic gates can include AND gates, OR gates, NOT gates, NANDgates, NOR gates, EXOR gates, EXNOR gates, or any combination thereof.An AND gate can produce a high output only if all the inputs are high.An OR gate can produce a high output if one or more of the inputs arehigh. A NOT gate can produce an inverted version of the input as anoutput, such as outputting a high value when the input is low. A NAND(NOT-AND) gate can produce an inverted AND output, such that the outputwill be high if any of the inputs are low. A NOR (NOT-OR) gate canproduce an inverted OR output, such that the NOR gate output is low ifany of the inputs are high. An EXOR (Exclusive-OR) gate can produce ahigh output if either, but not both, inputs are high. An EXNOR(Exclusive-NOR) gate can produce an inverted EXOR output, such that theoutput is low if either, but not both, inputs are high.

TABLE 1 Logic Gates Truth Table INPUTS OUTPUTS A B NOT A AND NAND OR NOREXOR EXNOR 0 0 1 0 1 0 1 0 1 0 1 1 0 1 1 0 1 0 1 0 0 0 1 1 0 1 0 1 1 0 10 1 0 0 1

One of skill in the art would appreciate that the logic gates can beused in various combinations to perform comparisons, arithmeticoperations, and the like. Further, one of skill in the art wouldappreciate how to sequence the use of various combinations of logicgates to perform complex processes, such as the processes describedherein.

In an example, a 1-bit binary comparison can be performed using a XNORgate since the result is high only when the two inputs are the same. Acomparison of two multi-bit values can be performed by using multipleXNOR gates to compare each pair of bits, and the combining the output ofthe XNOR gates using and AND gates, such that the result can be trueonly when each pair of bits have the same value. If any pair of bitsdoes not have the same value, the result of the corresponding XNOR gatecan be low, and the output of the AND gate receiving the low input canbe low.

In another example, a 1-bit adder can be implemented using a combinationof AND gates and XOR gates. Specifically, the 1-bit adder can receivethree inputs, the two bits to be added (A and B) and a carry bit (Cin),and two outputs, the sum (S) and a carry out bit (Cout). The Cin bit canbe set to 0 for addition of two one bit values, or can be used to couplemultiple 1-bit adders together to add two multi-bit values by receivingthe Cout from a lower order adder. In an exemplary embodiment, S can beimplemented by applying the A and B inputs to a XOR gate, and thenapplying the result and Cin to another XOR gate. Cout can be implementedby applying the A and B inputs to an AND gate, the result of the A-B XORfrom the SUM and the Cin to another AND, and applying the input of theAND gates to a XOR gate.

TABLE 2 1-bit Adder Truth Table INPUTS OUTPUTS A B Cin S Cout 0 0 0 0 01 0 0 0 1 0 1 0 0 1 1 1 0 1 0 0 0 1 0 1 1 0 1 1 0 0 1 1 1 0 1 1 1 1 1

In various embodiments, computer system 400 can be coupled via bus 402to a display 412, such as a cathode ray tube (CRT) or liquid crystaldisplay (LCD), for displaying information to a computer user. An inputdevice 414, including alphanumeric and other keys, can be coupled to bus402 for communicating information and command selections to processor404. Another type of user input device is a cursor control 416, such asa mouse, a trackball or cursor direction keys for communicatingdirection information and command selections to processor 404 and forcontrolling cursor movement on display 412. This input device typicallyhas two degrees of freedom in two axes, a first axis (i.e., x) and asecond axis (i.e., y), that allows the device to specify positions in aplane.

A computer system 400 can perform the present teachings. Consistent withcertain implementations of the present teachings, results can beprovided by computer system 400 in response to processor 404 executingone or more sequences of one or more instructions contained in memory406. Such instructions can be read into memory 406 from anothercomputer-readable medium, such as storage device 410. Execution of thesequences of instructions contained in memory 406 can cause processor404 to perform the processes described herein. In various embodiments,instructions in the memory can sequence the use of various combinationsof logic gates available within the processor to perform the processesdescribe herein. Alternatively hard-wired circuitry can be used in placeof or in combination with software instructions to implement the presentteachings. In various embodiments, the hard-wired circuitry can includethe necessary logic gates, operated in the necessary sequence to performthe processes described herein. Thus implementations of the presentteachings are not limited to any specific combination of hardwarecircuitry and software.

The term “computer-readable medium” as used herein refers to any mediathat participates in providing instructions to processor 404 forexecution. Such a medium can take many forms, including but not limitedto, non-volatile media, volatile media, and transmission media. Examplesof non-volatile media can include, but are not limited to, optical ormagnetic disks, such as storage device 410. Examples of volatile mediacan include, but are not limited to, dynamic memory, such as memory 406.Examples of transmission media can include, but are not limited to,coaxial cables, copper wire, and fiber optics, including the wires thatcomprise bus 402.

Common forms of non-transitory computer-readable media include, forexample, a floppy disk, a flexible disk, hard disk, magnetic tape, orany other magnetic medium, a CD-ROM, any other optical medium, punchcards, paper tape, any other physical medium with patterns of holes, aRAM, PROM, and EPROM, a FLASH-EPROM, any other memory chip or cartridge,or any other tangible medium from which a computer can read.

In accordance with various embodiments, instructions configured to beexecuted by a processor to perform a method are stored on acomputer-readable medium. The computer-readable medium can be a devicethat stores digital information. For example, a computer-readable mediumincludes a compact disc read-only memory (CD-ROM) as is known in the artfor storing software. The computer-readable medium is accessed by aprocessor suitable for executing instructions configured to be executed.

In various embodiments, the methods of the present teachings may beimplemented in a software program and applications written inconventional programming languages such as C, C++, C#, etc.

While the present teachings are described in conjunction with variousembodiments, it is not intended that the present teachings be limited tosuch embodiments. On the contrary, the present teachings encompassvarious alternatives, modifications, and equivalents, as will beappreciated by those of skill in the art.

Further, in describing various embodiments, the specification may havepresented a method and/or process as a particular sequence of steps.However, to the extent that the method or process does not rely on theparticular order of steps set forth herein, the method or process shouldnot be limited to the particular sequence of steps described. As one ofordinary skill in the art would appreciate, other sequences of steps maybe possible. Therefore, the particular order of the steps set forth inthe specification should not be construed as limitations on the claims.In addition, the claims directed to the method and/or process should notbe limited to the performance of their steps in the order written, andone skilled in the art can readily appreciate that the sequences may bevaried and still remain within the spirit and scope of the variousembodiments.

The embodiments described herein, can be practiced with other computersystem configurations including hand-held devices, microprocessorsystems, microprocessor-based or programmable consumer electronics,minicomputers, mainframe computers and the like. The embodiments canalso be practiced in distributing computing environments where tasks areperformed by remote processing devices that are linked through anetwork.

It should also be understood that the embodiments described herein canemploy various computer-implemented operations involving data stored incomputer systems. These operations are those requiring physicalmanipulation of physical quantities. Usually, though not necessarily,these quantities take the form of electrical or magnetic signals capableof being stored, transferred, combined, compared, and otherwisemanipulated. Further, the manipulations performed are often referred toin terms, such as producing, identifying, determining, or comparing.

Any of the operations that form part of the embodiments described hereinare useful machine operations. The embodiments, described herein, alsorelate to a device or an apparatus for performing these operations. Thesystems and methods described herein can be specially constructed forthe required purposes or it may be a general purpose computerselectively activated or configured by a computer program stored in thecomputer. In particular, various general purpose machines may be usedwith computer programs written in accordance with the teachings herein,or it may be more convenient to construct a more specialized apparatusto perform the required operations.

Certain embodiments can also be embodied as computer readable code on acomputer readable medium. The computer readable medium is any datastorage device that can store data, which can thereafter be read by acomputer system. Examples of the computer readable medium include harddrives, network attached storage (NAS), read-only memory, random-accessmemory, CD-ROMs, CD-Rs, CD-RWs, magnetic tapes, and other optical andnon-optical data storage devices. The computer readable medium can alsobe distributed over a network coupled computer systems so that thecomputer readable code is stored and executed in a distributed fashion.

Results

The mass analyzer is calibrated using MS Grade Perfluorotributylamine(PFTBA) from SynQuest Labs, Alachua, Fla. The PFTBA calibration compoundproduces ions having theoretical masses of 68.99466, 99.99306,130.99147, 263.98656, 413.97698, and 501.97059. A mixture ofbromobiphenyl ethers from tri- to deca- (from Sigma-Aldrich, St Louis,Mo.) is analyzed.

FIG. 5 shows an experimental mass spectrum of the bromobiphenyl ethersusing the calibration derived from the PFTBA calibration compound ascompared to a theoretical mass spectrum of the bromobiphenyl ethers. Theerror in the experimentally determined mass at m/z 959.16751 is 9 ppm.The data are tabulated in Table 1. FIG. 6 is a graph of the mass errorsas a function of m/z ratio. The mass errors are stable within the m/zrange covered by the PFTBA calibration compound, but increase as the m/zratio moves further from the calibration range.

TABLE 1 Theoretical Calculated m/z m/z Error PFTBA 68.9946612 68.994680.272484851 PFTBA 99.9930644 99.99311 0.456031629 PFTBA 130.9914676130.99152 0.400026055 PFTBA 263.9865576 263.98669 0.501540689 PFTBA413.9769768 413.97716 0.442536688 PFTBA 501.9705896 501.970930.678127379 Tribromobiphenyl ether 405.80211 405.80235 0.591421272Tetrabromobiphenyl ether 485.71057 485.71043 −0.288237499Pentabromobiphenyl ether 563.62109 563.62161 0.922605646Hexabromobiphenyl ether 643.52955 643.53089 2.082266463Heptabromobiphenyl ether 721.44006 721.44271 3.673208832Decabromobiphenyl ether 959.16751 959.17617 9.028662783 RMS (ppm)2.915169831 Max (ppm) 9.028662783

FIG. 7 shows an experimental mass spectrum of the bromobiphenyl ethersusing the calibration derived from the PFTBA calibration compound anddecabromobiphenyl ether in the sample as compared to a theoretical massspectrum of the bromobiphenyl ethers. The error in the experimentallydetermined mass at m/z 959.16751 is 0.8 ppm. The data are tabulated inTable 2. FIG. 8 is a graph of the mass errors as a function of m/zratio. FIG. 8 compares the mass error curve from FIG. 6 (masscalibration with PFTBA only) to the mass error curve for multiple runscalibrated using the PFTBA calibration compound and the decabromobphenylether within the sample. The mass errors when using both PFTBA anddecabromobphenyl ether are relatively consistent across the measured m/zrange. Although, the errors tend to be negative and the masses tend tobe systematically underestimated for these samples.

TABLE 2 Theoretical Calculated m/z m/z Error (ppm) PFTBA 68.994661268.99465 −0.162331401 PFTBA 99.9930644 99.993 −0.644044668 PFTBA130.9914676 130.99142 −0.363382447 PFTBA 263.9865576 263.9864−0.597000095 PFTBA 413.9769768 413.97684 −0.33045316 PFTBA 501.9705896501.97021 −0.756219603 Tribromobiphenyl ether 405.80211 405.80211 0Tetrabromobiphenyl ether 485.71057 485.70997 −1.235303568Pentabromobiphenyl ether 563.62109 563.62089 −0.354848325Hexabromobiphenyl ether 643.52955 643.52884 −1.103290439Heptabromobiphenyl ether 721.44006 721.43883 −1.704923345Decabromobiphenyl ether 959.16751 959.16673 −0.813205193 RMS (ppm)0.818936131 Max (ppm) −1.704923345

FIG. 9 shows an experimental mass spectrum of the bromobiphenyl ethersusing the calibration derived from the PFTBA calibration compound anddecabromobiphenyl ether and using decabromobiphenyl ether as a lock massas compared to a theoretical mass spectrum of the bromobiphenyl ethers.The error in the experimentally determined mass at m/z 959.16751 is 0.3ppm. The data are tabulated in Table 3. FIG. 10 is a graph of the masserrors as a function of m/z ratio. FIG. 10 compares the mass error curvefrom FIG. 6 (mass calibration with PFTBA only) to the mass error curvefor multiple runs when the PFTBA calibration compound and thedecabromobphenyl ether are used for the calibration curve anddecabromobphenyl ether (alone or in combination with Heptabromobiphenylether) is used as a lock mass. The mass errors when using both PFTBA anddecabromobphenyl ether along with a lock mass are relatively consistentacross the measured m/z range.

TABLE 3 Theoretical Calculated m/z m/z Error (ppm) PFTBA 68.994661268.99468 0.272484851 PFTBA 99.9930644 99.99308 0.15601082 PFTBA130.9914676 130.99145 −0.134359896 PFTBA 263.9865576 263.986610.198494955 PFTBA 413.9769768 413.97711 0.321757024 PFTBA 501.9705896501.97086 0.538676978 Tribromobiphenyl ether 405.80211 405.80188−0.566778719 Tetrabromobiphenyl ether 485.71057 485.71037 −0.411767856Pentabromobiphenyl ether 563.62109 563.62111 0.035484833Hexabromobiphenyl ether 643.52955 643.52919 −0.559414871Heptabromobiphenyl ether 721.44006 721.43969 −0.51286312Decabromobiphenyl ether 959.16751 959.16782 0.323196936 RMS (ppm)0.378838198 Max (ppm) −0.566778719

What is claimed is:
 1. A method comprising: producing ions from one ormore calibrant species and delivering the ions to a mass analyzer;measuring a first set of mass related physical values for the ions fromthe one or more calibrant species; producing ions from a sample anddelivering the ions to a mass analyzer, the sample including a firstsample ion species of known mass, the first sample ion species having amass-to-charge ratio outside of the range of the mass-to-charge ratiosof the calibrant ion species, wherein producing ions from the sampleoccurs separately from producing ions from the one or more calibrantspecies; measuring a second mass related physical value for the firstsample ion species; calculating a mass calibration curve based on thefirst set of mass related physical values for the plurality calibrantion species and second mass related physical value for the first sampleion species; and modifying at least one instrument parameter based onthe mass calibration curve.
 2. The method of claim 1, wherein the massanalyzer includes a Fourier transform mass analyzer, and the instrumentparameter is selected from the group consisting of a coefficientrelating m/z to ion frequency, a frequency range for an image current, adigitizing rate, a filter bandwidth for an image current, and anycombination thereof.
 3. The method of claim 1, wherein the mass analyzerincludes a quadrupole mass analyzer or a quadrupole ion trap massanalyzer, and the instrument parameter is selected from the groupconsisting of an RF voltage, a DC voltage, and any combination thereof.4. The method of claim 1, wherein the mass analyzer includes atime-of-flight mass analyzer, and the instrument parameter is selectedfrom the group consisting of a coefficient relating m/z to flight time,an acquisition time window, a flight tube clearing pulse time, and anycombination thereof.
 5. The method of claim 1, wherein the sample isprovided by a gas chromatographic instrument or a liquid chromatographicinstrument.
 6. The method of claim 1, further comprising: providing asecond sample to the mass spectrometer, the sample including a secondsample ion species; operating the mass spectrometer using the modifiedinstrument parameter from the calibration; and measuring a third massrelated physical value for the second sample ion species.
 7. The methodof claim 6, further comprising: shifting the mass calibration curvebased on a measured mass-to-charge ratio of a third sample ion specieswithin the second sample to account for scan specific drifts in the masscalibration curve, wherein the instrument parameter is not changed basedon the shifting of the mass calibration curve.
 8. The method of claim 6,wherein the second sample ion species has a mass-to-charge ratio withinthe range of the mass-to-charge ratio of the first sample ion speciesand the mass-to-charge ratio of at least one of the calibrant ionspecies.
 9. The method of claim 1, wherein the first sample ion specieshas a mass-to-charge ratio above the range of the mass-to-charge ratiosof the calibrant ion species.
 10. The method of claim 1, wherein thefirst sample ion species has a mass-to-charge ratio below the range ofthe mass-to-charge ratios of the calibrant ion species.
 11. The methodof claim 1, wherein producing ions from the sample occurs at a differenttime from producing ions from the one or more calibrant species.
 12. Amass spectrometer, comprising: an ion source configured to form ionsfrom one or more calibrant species and to separately form ions from asample, the sample including a first sample ion species of known mass,the first sample ion species having a mass-to-charge ratio outside ofthe range of the mass-to-charge ratios of the calibrant ion species; amass analyzer configured to measure a mass related physical value for anion; a controller configured to: obtain a first set of mass relatedphysical values for ions from the one or more calibrant species; obtaina second mass related physical value for the first sample ion species;calculate a mass calibration curve based on the first set of massrelated physical values, the second mass related physical value, andknown mass-to-charge ratios of the ions from the one or more calibrantspecies and the first sample ion species; and modify at least oneinstrument parameter of the mass analyzer based on the mass calibrationcurve.
 13. The mass spectrometer of claim 12, wherein the mass analyzerincludes a Fourier transform mass analyzer, and modifying the operationof the mass analyzer includes modifying a coefficient relating m/z toion frequency, a frequency range for an image current, a digitizingrate, a filter bandwidth for an image current, and any combinationthereof.
 14. The mass spectrometer of claim 12, wherein the massanalyzer includes a quadrupole mass analyzer or a quadrupole ion trapmass analyzer, and modifying the operation of the mass analyzer includesmodifying an RF voltage, a DC voltage, or any combination thereof. 15.The mass spectrometer of claim 12, wherein the mass analyzer includes atime-of-flight mass analyzer, and modifying the operation of the massanalyzer includes modifying a coefficient relating m/z to flight time,an acquisition time window, a flight tube clearing pulse time, or anycombination thereof.
 16. The mass spectrometer of claim 12, wherein themass spectrometer further includes a gas chromatograph or a liquidchromatograph for supplying the sample to the ion source.
 17. The massspectrometer of claim 12, wherein the controller is further configuredto: operate the ion source to provide a second sample to the massspectrometer, the sample including a second sample ion species; operatethe mass spectrometer using the modified instrument parameter from thecalibration; and obtain a third set of mass related physical values forthe second sample ion species.
 18. The mass spectrometer of claim 12,wherein the first sample ion species has a mass-to-charge ratio abovethe range of the mass-to-charge ratios of the calibrant ion species. 19.The mass spectrometer of claim 12, wherein the first sample ion specieshas a mass-to-charge ratio below the range of the mass-to-charge ratiosof the calibrant ion species.
 20. The mass spectrometer of claim 12,wherein the ion source is configured to form ions from one or morecalibrant species at a different time from ions from a sample.